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- PDB-4xf4: Cysteine dioxygenase at pH 8.0 in complex with homocysteine -

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Basic information

Entry
Database: PDB / ID: 4xf4
TitleCysteine dioxygenase at pH 8.0 in complex with homocysteine
ComponentsCysteine dioxygenase type 1
KeywordsOXIDOREDUCTASE / Cupin Fold / cysteine to cysteine sulfinic acid catalysis / thiol dioxygenase
Function / homology
Function and homology information


L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid ...L-cysteine metabolic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / cysteine metabolic process / response to glucagon / nickel cation binding / response to amino acid / response to glucocorticoid / response to cAMP / lactation / ferrous iron binding / response to ethanol / zinc ion binding / cytosol
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3485 Å
AuthorsDriggers, C.M. / Karplus, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH-DK-056649 United States
Department of Energy (DOE, United States)DE-AC02-98CH10886 United States
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structure-Based Insights into the Role of the Cys-Tyr Crosslink and Inhibitor Recognition by Mammalian Cysteine Dioxygenase.
Authors: Driggers, C.M. / Kean, K.M. / Hirschberger, L.L. / Cooley, R.B. / Stipanuk, M.H. / Karplus, P.A.
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2503
Polymers23,0591
Non-polymers1912
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 57.600, 122.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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Components

#1: Protein Cysteine dioxygenase type 1 / Cysteine dioxygenase type I / CDO-I


Mass: 23058.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cdo1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21816, cysteine dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M tri-sodium citrate pH=5.6, 24% PEG 4000, 0.15M ammonium acetate. 1:1 drop ratio with microseeding.; Soak solution at pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2014
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.3485→41 Å / Num. all: 43919 / Num. obs: 43838 / % possible obs: 94.9 % / Redundancy: 23.8 % / Net I/σ(I): 23.7
Reflection shellResolution: 1.3485→1.37 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1 / % possible all: 68

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ieu

4ieu


Resolution: 1.3485→40.729 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 4306 9.82 %same 5% as 4ieu
Rwork0.1624 ---
obs0.1652 43838 94.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3485→40.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 9 280 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111683
X-RAY DIFFRACTIONf_angle_d1.3582293
X-RAY DIFFRACTIONf_dihedral_angle_d13.486632
X-RAY DIFFRACTIONf_chiral_restr0.083243
X-RAY DIFFRACTIONf_plane_restr0.006304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3485-1.36380.36831100.3248894X-RAY DIFFRACTION67
1.3638-1.37980.3226920.3102972X-RAY DIFFRACTION69
1.3798-1.39670.33651040.29181013X-RAY DIFFRACTION75
1.3967-1.41440.26561090.30111064X-RAY DIFFRACTION77
1.4144-1.4330.29691170.27771123X-RAY DIFFRACTION81
1.433-1.45260.28551130.26111167X-RAY DIFFRACTION86
1.4526-1.47340.26221420.24991237X-RAY DIFFRACTION91
1.4734-1.49530.26021440.22351295X-RAY DIFFRACTION96
1.4953-1.51870.25031580.2111365X-RAY DIFFRACTION99
1.5187-1.54360.23711490.18861347X-RAY DIFFRACTION100
1.5436-1.57020.20161730.18951358X-RAY DIFFRACTION100
1.5702-1.59880.1991560.16541369X-RAY DIFFRACTION100
1.5988-1.62950.17311300.16851397X-RAY DIFFRACTION100
1.6295-1.66280.19171570.15721349X-RAY DIFFRACTION100
1.6628-1.6990.18741510.16781387X-RAY DIFFRACTION100
1.699-1.73850.17161600.16341361X-RAY DIFFRACTION100
1.7385-1.7820.18551510.17221364X-RAY DIFFRACTION100
1.782-1.83010.19951410.16461400X-RAY DIFFRACTION100
1.8301-1.8840.20671330.15691406X-RAY DIFFRACTION100
1.884-1.94480.19381370.16211397X-RAY DIFFRACTION100
1.9448-2.01430.18391690.15441377X-RAY DIFFRACTION100
2.0143-2.09490.17751750.15591358X-RAY DIFFRACTION100
2.0949-2.19030.18271360.15261423X-RAY DIFFRACTION100
2.1903-2.30580.181400.14661427X-RAY DIFFRACTION100
2.3058-2.45020.19421460.1541390X-RAY DIFFRACTION100
2.4502-2.63930.19751620.15811419X-RAY DIFFRACTION100
2.6393-2.90490.19951670.16021411X-RAY DIFFRACTION100
2.9049-3.32510.17111560.15761425X-RAY DIFFRACTION100
3.3251-4.18860.18331590.14381464X-RAY DIFFRACTION100
4.1886-40.74790.16681690.14911573X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2038 Å / Origin y: 3.0968 Å / Origin z: -49.5634 Å
111213212223313233
T0.0598 Å2-0.0003 Å2-0.0024 Å2-0.0824 Å20.0029 Å2--0.072 Å2
L0.9164 °20.4312 °2-0.1857 °2-0.8816 °20.0919 °2--0.8067 °2
S0.0209 Å °-0.0105 Å °-0.0385 Å °0.0262 Å °-0.0139 Å °-0.0096 Å °0.0443 Å °-0.0336 Å °-0.0003 Å °
Refinement TLS groupSelection details: chain 'A' and resid 5 through 190

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